Consider making your scatter points transparent. You can do this by passing an alpha keyword to plt.scatter. Here's an example, modified from mplot3dexample gallery, with alpha = 1.0, which is the default value:

ax.scatter(xs, ys, zs, alpha=1.0, s=0.2)

And here is the same scatter point cloud drawn with alpha = 0.1:

ax.scatter(xs, ys, zs, alpha=0.1, s=0.2)

Note that while this appears to be a good visualization, the interactive part of it is quite slow for a large number of points. If you really need fast performance, consider an alternative approach - splitting the lines in segments and coloring them by index, similarly to what's being done here.

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